Menu item for new client appears under the root of navigation menu, not under Support tickets

Menu items for newly created clients usually appeared under Support tickets, so the menu looked like:

|___Support tickets
      |___Old Client
      |___New Client

For some reason now it started to menu items for new clients under central root like:

|___Support tickets
|      |___Old Client
|      |___Old Client
|___New Client
|___Another New Client

I have reset all the menu items, however it does not help - it continues to add to root of Navigation menu. How can I fix this?